- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 69a870: Fix modules resolver (addition of the resolver_msg...
by GitHub 21 Sep '17

21 Sep '17

Branch: refs/heads/release_16.07 Home: https://github.com/galaxyproject/galaxy Commit: 69a87003f70e3925554fcc88fd2080edab619ed1 https://github.com/galaxyproject/galaxy/commit/69a87003f70e3925554fcc88fd20… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-09-20 (Wed, 20 Sep 2017) Changed paths: M lib/galaxy/tools/deps/resolvers/modules.py Log Message: ----------- Fix modules resolver (addition of the resolver_msg property on the base class references name and version attributes that were not defined in the ModuleDependecy). Commit: 2ffeedfa723cae9252bda2098918df82daf9cf41 https://github.com/galaxyproject/galaxy/commit/2ffeedfa723cae9252bda2098918… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-09-21 (Thu, 21 Sep 2017) Changed paths: M lib/galaxy/tools/deps/resolvers/modules.py Log Message: ----------- Merge pull request #4663 from natefoo/fix-modules-resolver [16.07] Fix modules resolver Compare: https://github.com/galaxyproject/galaxy/compare/4345d8e7d7a3...2ffeedfa723c

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[galaxyproject/usegalaxy-playbook] 92278f: Fix metadata on Main until we have 17.09
by GitHub 21 Sep '17

21 Sep '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 92278f434d7e56312b18c1cc78e332e34648507f https://github.com/galaxyproject/usegalaxy-playbook/commit/92278f434d7e5631… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-09-21 (Thu, 21 Sep 2017) Changed paths: M env/main/templates/galaxy/config/job_conf.xml.j2 Log Message: ----------- Fix metadata on Main until we have 17.09

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[galaxyproject/usegalaxy-playbook] b2c1b7: Fixes for modified destination names
by GitHub 21 Sep '17

21 Sep '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: b2c1b7744a625a565c84d33493314498e61dda54 https://github.com/galaxyproject/usegalaxy-playbook/commit/b2c1b7744a625a56… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-09-21 (Thu, 21 Sep 2017) Changed paths: M env/main/templates/galaxy/config/job_conf.xml.j2 M env/test/templates/galaxy/config/job_conf.xml.j2 Log Message: ----------- Fixes for modified destination names

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[galaxyproject/galaxy] 095307: Selenium fixes for publishing histories button.
by GitHub 21 Sep '17

21 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 095307b6783f39bce7a1f4c6fbb4e603e368ecfb https://github.com/galaxyproject/galaxy/commit/095307b6783f39bce7a1f4c6fbb4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-20 (Wed, 20 Sep 2017) Changed paths: M test/selenium_tests/test_published_histories_grid.py Log Message: ----------- Selenium fixes for publishing histories button. Fixes https://jenkins.galaxyproject.org/job/selenium/488/testReport/junit/seleniu…. It looks like a Toastr popup sometimes intercepts the click, this should solve that I believe. Commit: 98f2c108238e07a5379712f22ed8c46467204de6 https://github.com/galaxyproject/galaxy/commit/98f2c108238e07a5379712f22ed8… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-09-21 (Thu, 21 Sep 2017) Changed paths: M test/selenium_tests/test_published_histories_grid.py Log Message: ----------- Merge pull request #4660 from jmchilton/selenium_fixes_30 Selenium fixes for publishing histories button. Compare: https://github.com/galaxyproject/galaxy/compare/87d5d440238e...98f2c108238e

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[galaxyproject/galaxy] ac10e0: Reload tools if a macro changes
by GitHub 21 Sep '17

21 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ac10e0d2245ed9bfec4893512fb1d46532654146 https://github.com/galaxyproject/galaxy/commit/ac10e0d2245ed9bfec4893512fb1… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-19 (Tue, 19 Sep 2017) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/cache.py M lib/galaxy/tools/parser/factory.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/parser/yaml.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/util/xml_macros.py M scripts/validate_tools.sh M test/unit/tools/test_tool_loader.py M test/unit/tools/test_toolbox.py M test/unit/tools_support.py Log Message: ----------- Reload tools if a macro changes We do this by recording any macros that are required to load a tool. When loading a tool we register the macro to be watched, and if the macro changes we reload all corresponding tools. Commit: d3d134030aded5b29e62c4c1d5946f3266a34827 https://github.com/galaxyproject/galaxy/commit/d3d134030aded5b29e62c4c1d594… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-21 (Thu, 21 Sep 2017) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/loader.py M lib/galaxy/tools/parser/factory.py M lib/galaxy/util/xml_macros.py M scripts/validate_tools.sh M test/unit/tools/test_tool_loader.py Log Message: ----------- Rework #4635 to preserve backward compatibility on modules shared via galaxy-lib. Also cleanup comments and such in xml_macros to reflect this doesn't apply just to tools. Commit: 87d5d440238e1ce7f1aaaeb152bc00ecf1f6faf1 https://github.com/galaxyproject/galaxy/commit/87d5d440238e1ce7f1aaaeb152bc… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-21 (Thu, 21 Sep 2017) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/cache.py M lib/galaxy/tools/loader.py M lib/galaxy/tools/parser/factory.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/parser/yaml.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/util/xml_macros.py M test/unit/tools/test_tool_loader.py M test/unit/tools/test_toolbox.py M test/unit/tools_support.py Log Message: ----------- Merge pull request #4635 from mvdbeek/reload_on_macro_changes Reload tools if a macro changes Compare: https://github.com/galaxyproject/galaxy/compare/e057d7d88700...87d5d440238e

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[galaxyproject/usegalaxy-playbook] 68cc4c: Use remote datatypes_conf.xml for Main Pulsar unti...
by GitHub 21 Sep '17

21 Sep '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 68cc4c1373c32a927a44f3c8d640fc790493c6d7 https://github.com/galaxyproject/usegalaxy-playbook/commit/68cc4c1373c32a92… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-09-21 (Thu, 21 Sep 2017) Changed paths: M env/main/templates/galaxy/config/job_conf.xml.j2 Log Message: ----------- Use remote datatypes_conf.xml for Main Pulsar until bugfixes are merged and we update

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[galaxyproject/galaxy] 0730d5: Move serving plugins and related code to the same ...
by GitHub 21 Sep '17

21 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0730d55c0d97776cd30ecd1882b2898fa96f00ab https://github.com/galaxyproject/galaxy/commit/0730d55c0d97776cd30ecd1882b2… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-09-14 (Thu, 14 Sep 2017) Changed paths: A lib/galaxy/visualization/plugins/interactive_environments.py M lib/galaxy/visualization/plugins/plugin.py A lib/galaxy/visualization/plugins/pluginframework.py M lib/galaxy/visualization/plugins/registry.py R lib/galaxy/web/base/interactive_environments.py R lib/galaxy/web/base/pluginframework.py Log Message: ----------- Move serving plugins and related code to the same directory Commit: acd964299f21052d90d8fd49bcf3af7b4baa8191 https://github.com/galaxyproject/galaxy/commit/acd964299f21052d90d8fd49bcf3… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-09-14 (Thu, 14 Sep 2017) Changed paths: M lib/galaxy/visualization/plugins/pluginframework.py M lib/galaxy/visualization/plugins/registry.py Log Message: ----------- Use underscores for private functions Commit: 88d8e4b369379253a4245123edacc37aacc985b8 https://github.com/galaxyproject/galaxy/commit/88d8e4b369379253a4245123edac… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-09-14 (Thu, 14 Sep 2017) Changed paths: M lib/galaxy/visualization/plugins/pluginframework.py Log Message: ----------- Remove unused hook plugin manager Commit: 6840d8666449b07c4c664c14d404332614895b7f https://github.com/galaxyproject/galaxy/commit/6840d8666449b07c4c664c14d404… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-09-14 (Thu, 14 Sep 2017) Changed paths: M lib/galaxy/visualization/plugins/pluginframework.py Log Message: ----------- Rename private functions Commit: bf21708710eaf9a5f19587f4b0659b41079adfcf https://github.com/galaxyproject/galaxy/commit/bf21708710eaf9a5f19587f4b065… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-09-14 (Thu, 14 Sep 2017) Changed paths: M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/visualization/plugins/pluginframework.py Log Message: ----------- Move base plugin to viz plugin Commit: e5e2a986c96967d932961dbbadf32d61f2581fd3 https://github.com/galaxyproject/galaxy/commit/e5e2a986c96967d932961dbbadf3… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-09-14 (Thu, 14 Sep 2017) Changed paths: M lib/galaxy/visualization/plugins/pluginframework.py Log Message: ----------- Remove unused exception types Commit: 8e83ee3f0eeb69b262e05aa80ee19199b8502858 https://github.com/galaxyproject/galaxy/commit/8e83ee3f0eeb69b262e05aa80ee1… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-09-14 (Thu, 14 Sep 2017) Changed paths: M lib/galaxy/visualization/plugins/pluginframework.py Log Message: ----------- Call directory handler in viz manager, similar to tours and webhooks Commit: 881e5cd1cb11d0a8723e41af6f7bf41e6d2e1d3d https://github.com/galaxyproject/galaxy/commit/881e5cd1cb11d0a8723e41af6f7b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-09-14 (Thu, 14 Sep 2017) Changed paths: M lib/galaxy/visualization/plugins/pluginframework.py Log Message: ----------- Remove unused exception and base initialization Commit: 50577e45c9f7148c8f169e2cc9212cda6ea052f0 https://github.com/galaxyproject/galaxy/commit/50577e45c9f7148c8f169e2cc921… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-09-14 (Thu, 14 Sep 2017) Changed paths: M lib/galaxy/visualization/plugins/pluginframework.py Log Message: ----------- Move viz specific is plugin check and load plugin to serving plugin manager Commit: f867236bce8405c514e640d650d7c8910f4abe1b https://github.com/galaxyproject/galaxy/commit/f867236bce8405c514e640d650d7… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-09-14 (Thu, 14 Sep 2017) Changed paths: M lib/galaxy/visualization/plugins/pluginframework.py Log Message: ----------- Remove base plugin manager inheritance Commit: ce7da0ccc24c5ce65d57b7f273d0991af44b7f20 https://github.com/galaxyproject/galaxy/commit/ce7da0ccc24c5ce65d57b7f273d0… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-09-14 (Thu, 14 Sep 2017) Changed paths: M lib/galaxy/visualization/plugins/pluginframework.py Log Message: ----------- Remove unused plugin check caller Commit: c44057dacdcfbc061fe43288babaef2b994ec303 https://github.com/galaxyproject/galaxy/commit/c44057dacdcfbc061fe43288baba… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-09-14 (Thu, 14 Sep 2017) Changed paths: M lib/galaxy/visualization/plugins/pluginframework.py Log Message: ----------- Remove unused load plugin from page serving manager Commit: 241bc43f79a86e071c738aaa9f6735ca298ee6aa https://github.com/galaxyproject/galaxy/commit/241bc43f79a86e071c738aaa9f67… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-09-14 (Thu, 14 Sep 2017) Changed paths: M lib/galaxy/visualization/plugins/pluginframework.py Log Message: ----------- Fix init parameters Commit: 854ce2df03de4bb1e9bb979ba24b973e18016f97 https://github.com/galaxyproject/galaxy/commit/854ce2df03de4bb1e9bb979ba24b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-09-14 (Thu, 14 Sep 2017) Changed paths: R lib/galaxy/visualization/plugins/pluginframework.py M lib/galaxy/visualization/plugins/registry.py Log Message: ----------- Move page serving plugin manager to visualization registry Commit: 6131db81d2144aff074f19d0da73db65d4fc9359 https://github.com/galaxyproject/galaxy/commit/6131db81d2144aff074f19d0da73… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-09-14 (Thu, 14 Sep 2017) Changed paths: M lib/galaxy/visualization/plugins/registry.py Log Message: ----------- Fix inheritance Commit: 769e4f7d9e223b75be1338e3ce73bcc5b1c79405 https://github.com/galaxyproject/galaxy/commit/769e4f7d9e223b75be1338e3ce73… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-09-14 (Thu, 14 Sep 2017) Changed paths: M lib/galaxy/visualization/plugins/registry.py Log Message: ----------- Remove unused static url caller Commit: 15b18286c4001f3d2194df32c04482e51130a37a https://github.com/galaxyproject/galaxy/commit/15b18286c4001f3d2194df32c044… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-09-14 (Thu, 14 Sep 2017) Changed paths: M lib/galaxy/visualization/plugins/registry.py Log Message: ----------- Fold page serving manager into visualization registry Commit: 60fd32487c63f16c11ed969c1e44b0967c150aad https://github.com/galaxyproject/galaxy/commit/60fd32487c63f16c11ed969c1e44… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-09-14 (Thu, 14 Sep 2017) Changed paths: M lib/galaxy/visualization/plugins/registry.py Log Message: ----------- Fix comment Commit: 724ebdb4bf8faf26db586dffbee42bad6fd362a4 https://github.com/galaxyproject/galaxy/commit/724ebdb4bf8faf26db586dffbee4… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-09-14 (Thu, 14 Sep 2017) Changed paths: M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/visualization/plugins/registry.py Log Message: ----------- Remove plugin framework imports Commit: 5a3595afad56e09307c43ab2723b9faa596dd3a6 https://github.com/galaxyproject/galaxy/commit/5a3595afad56e09307c43ab2723b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-09-14 (Thu, 14 Sep 2017) Changed paths: M lib/galaxy/visualization/plugins/plugin.py Log Message: ----------- Fold base viz plugin into viz plugin Commit: e414dc2c52f2bf7b10fa9e40ebd29595ea0e58a8 https://github.com/galaxyproject/galaxy/commit/e414dc2c52f2bf7b10fa9e40ebd2… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-09-14 (Thu, 14 Sep 2017) Changed paths: M lib/galaxy/visualization/plugins/plugin.py Log Message: ----------- Consolidate comments Commit: 8492136dfdcf293d739fc0a88666ecff46965222 https://github.com/galaxyproject/galaxy/commit/8492136dfdcf293d739fc0a88666… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-09-14 (Thu, 14 Sep 2017) Changed paths: M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/visualization/plugins/registry.py Log Message: ----------- Fix import styles and order Commit: 28bda0c62efd37faeb96323d7d56b15cf418f1d0 https://github.com/galaxyproject/galaxy/commit/28bda0c62efd37faeb96323d7d56… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-09-14 (Thu, 14 Sep 2017) Changed paths: M lib/galaxy/visualization/plugins/registry.py Log Message: ----------- Remove unused template path handler from registry, its already called for the plugin Commit: 60cad0c3765441ae2cf990852ffaa533080503f5 https://github.com/galaxyproject/galaxy/commit/60cad0c3765441ae2cf990852ffa… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-09-14 (Thu, 14 Sep 2017) Changed paths: M lib/galaxy/visualization/plugins/registry.py Log Message: ----------- Use capital letter for constants Commit: 9a4175e0736355d7de821ac44772ec94723b7acc https://github.com/galaxyproject/galaxy/commit/9a4175e0736355d7de821ac44772… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-09-14 (Thu, 14 Sep 2017) Changed paths: M lib/galaxy/visualization/plugins/registry.py Log Message: ----------- Move constants Commit: f558970ef1b61bb8465dba699abf24323f41aa10 https://github.com/galaxyproject/galaxy/commit/f558970ef1b61bb8465dba699abf… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-09-14 (Thu, 14 Sep 2017) Changed paths: M lib/galaxy/visualization/plugins/registry.py Log Message: ----------- Remove unused custom base url option, handle plugin route same as for interactive environments Commit: d6dad603e8dce06c046ae726ae8893c26b89cf32 https://github.com/galaxyproject/galaxy/commit/d6dad603e8dce06c046ae726ae88… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-09-14 (Thu, 14 Sep 2017) Changed paths: M lib/galaxy/visualization/plugins/registry.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Remove unnecessary static path caller Commit: 3daae84408823ad35ce9001aef36ce85894fd3de https://github.com/galaxyproject/galaxy/commit/3daae84408823ad35ce9001aef36… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-09-14 (Thu, 14 Sep 2017) Changed paths: M lib/galaxy/visualization/plugins/registry.py Log Message: ----------- Remove unused template helper from previously inherited base class Commit: 2d4689a8f7dac2ca5ff21491aca771b8536b1a1e https://github.com/galaxyproject/galaxy/commit/2d4689a8f7dac2ca5ff21491aca7… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-09-14 (Thu, 14 Sep 2017) Changed paths: M lib/galaxy/visualization/plugins/registry.py Log Message: ----------- Remove unused fill template caller, this handled by the plugin itself not by the registry Commit: b6949ac56303194241009fe9a39922d9c40bbc73 https://github.com/galaxyproject/galaxy/commit/b6949ac56303194241009fe9a399… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-09-15 (Fri, 15 Sep 2017) Changed paths: M lib/galaxy/visualization/plugins/registry.py Log Message: ----------- Remove unused imports Commit: 9a3a9f6ae27e137de78e46bdbbc8c3847de69109 https://github.com/galaxyproject/galaxy/commit/9a3a9f6ae27e137de78e46bdbbc8… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-09-15 (Fri, 15 Sep 2017) Changed paths: R test/unit/web/base/__init__.py R test/unit/web/base/test_HookPluginManager.py R test/unit/web/base/test_PageServingPluginManager.py R test/unit/web/base/test_PluginManager.py Log Message: ----------- Remove test cases for unused plugin base classes Commit: e057d7d887006a7543196f6defb39e60876c14f2 https://github.com/galaxyproject/galaxy/commit/e057d7d887006a7543196f6defb3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-21 (Thu, 21 Sep 2017) Changed paths: A lib/galaxy/visualization/plugins/interactive_environments.py M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/visualization/plugins/registry.py R lib/galaxy/web/base/interactive_environments.py R lib/galaxy/web/base/pluginframework.py M lib/galaxy/webapps/galaxy/buildapp.py R test/unit/web/base/__init__.py R test/unit/web/base/test_HookPluginManager.py R test/unit/web/base/test_PageServingPluginManager.py R test/unit/web/base/test_PluginManager.py Log Message: ----------- Merge pull request #4620 from guerler/reduce_viz_framework Remove unused abstraction layers from Visualizations Registry Compare: https://github.com/galaxyproject/galaxy/compare/b369a1dc221f...e057d7d88700

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[galaxyproject/usegalaxy-playbook] 87aeec: Resource param adjustments for Main
by GitHub 21 Sep '17

21 Sep '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 87aeec73070c8a7bc075bb69696ece7aa9d26cd3 https://github.com/galaxyproject/usegalaxy-playbook/commit/87aeec73070c8a7b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-09-21 (Thu, 21 Sep 2017) Changed paths: M env/main/files/galaxy/config/job_resource_params_conf.xml Log Message: ----------- Resource param adjustments for Main Commit: 046261511e6afd679809044509c579294392343b https://github.com/galaxyproject/usegalaxy-playbook/commit/046261511e6afd67… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-09-21 (Thu, 21 Sep 2017) Changed paths: M env/main/templates/galaxy/config/job_conf.xml.j2 M env/test/templates/galaxy/config/job_conf.xml.j2 Log Message: ----------- Additional post-macroification fixes Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/996b99d22617...…

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[galaxyproject/galaxy] 3dbdf7: Make liftover tool use data table
by GitHub 21 Sep '17

21 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3dbdf7d4747cd036515466b314f4d654f7755905 https://github.com/galaxyproject/galaxy/commit/3dbdf7d4747cd036515466b314f4… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-19 (Tue, 19 Sep 2017) Changed paths: M tools/extract/liftOver_wrapper.xml Log Message: ----------- Make liftover tool use data table Commit: b369a1dc221feb8429cc69fe59d9f6311929719b https://github.com/galaxyproject/galaxy/commit/b369a1dc221feb8429cc69fe59d9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-21 (Thu, 21 Sep 2017) Changed paths: M tools/extract/liftOver_wrapper.xml Log Message: ----------- Merge pull request #4645 from mvdbeek/fix_liftover_tool Make liftover tool use data tables Compare: https://github.com/galaxyproject/galaxy/compare/669f944292ec...b369a1dc221f

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[galaxyproject/galaxy] a3ff12: Explicitly write registry.xml when creating a job ...
by GitHub 21 Sep '17

21 Sep '17

Branch: refs/heads/release_17.05 Home: https://github.com/galaxyproject/galaxy Commit: a3ff1297435721d3f687052382b75a2a2f2f9b25 https://github.com/galaxyproject/galaxy/commit/a3ff1297435721d3f687052382b7… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-19 (Tue, 19 Sep 2017) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Explicitly write registry.xml when creating a job for the upload tool Commit: d980dfa162b340423ffd8822ac9dcdf6f1997e80 https://github.com/galaxyproject/galaxy/commit/d980dfa162b340423ffd8822ac9d… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-19 (Tue, 19 Sep 2017) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Write registry.xml for all tools that require galaxy's python env This should cover the upload and data_source tools. Commit: b7b3ffb1813f31b7811bdbb35602743294356f66 https://github.com/galaxyproject/galaxy/commit/b7b3ffb1813f31b7811bdbb35602… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-19 (Tue, 19 Sep 2017) Changed paths: M test/unit/jobs/test_job_wrapper.py Log Message: ----------- Fix unit test failure Commit: 5d7b524b5785fcb483dbc7381c871595a070b1b0 https://github.com/galaxyproject/galaxy/commit/5d7b524b5785fcb483dbc7381c87… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-09-21 (Thu, 21 Sep 2017) Changed paths: M lib/galaxy/jobs/__init__.py M test/unit/jobs/test_job_wrapper.py Log Message: ----------- Merge pull request #4644 from mvdbeek/upload_tool_registry_xml_failure [17.05] BUG: Explicitly write registry.xml when creating a job for the upload tool Compare: https://github.com/galaxyproject/galaxy/compare/03d9a9c6fba0...5d7b524b5785

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